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Code Block
languagebash
titleYou can check this against the original fastq files SRR030257_1.fastq and SRR030257_1.fastq (check them in your GVA_bowtie2_mapping directory)
collapsetrue
grep -c "^+$" $SCRATCH/GVA_bowtie2_mapping/SRR030257_1.fastq
grep -c "^+$" $SCRATCH/GVA_bowtie2_mapping/SRR030257_12.fastq

While we haven't discussed sam format in much detail, each read gets its own line, and if you compare the .sam file and the original fastq file listed above, you see that each line on the sam file seems to start with 'SRR030257' followed by a number related to the read. This gives us a base handle to check with grep

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